Download MendeleyCrystal structure of a peptide-HLA complex
Gras, S., Rossjohn, J.To be published.
3SPV
Crystal structure of a peptide-HLA complex
- PDB DOI: https://doi.org/10.2210/pdb3SPV/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Human herpesvirus 4 strain B95-8
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-07-04 Released: 2012-07-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.219
- R-Value Work: 0.196
- R-Value Observed: 0.197
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HLA class I histocompatibility antigen, B-8 alpha chain | 276 | Homo sapiens | Mutation(s): 0 Gene Names: HLA-B |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01889 (Homo sapiens) Explore P01889 Go to UniProtKB: P01889 | |||||
PHAROS: P01889 GTEx: ENSG00000234745 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01889 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-2-microglobulin | 99 | Homo sapiens | Mutation(s): 0 Gene Names: B2M |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769 | |||||
PHAROS: P61769 GTEx: ENSG00000166710 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| peptide from Trans-activator protein BZLF1 | 8 | Human herpesvirus 4 strain B95-8 | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P03206 (Epstein-Barr virus (strain B95-8)) Explore P03206 Go to UniProtKB: P03206 | |||||
Entity Groups | |||||
| UniProt Group | P03206 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACT Query on ACT | D [auth A], E [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NA Query on NA | F [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.219
- R-Value Work: 0.196
- R-Value Observed: 0.197
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.56 | α = 90 |
| b = 81.46 | β = 90 |
| c = 110.02 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
Entry History
Deposition Data
- Released Date: 2012-07-04 Deposition Author(s): Gras, S., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2012-07-04
Type: Initial release - Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
